RetrogeneDB ID: retro_mmus_3443

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:44862879..44863722(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083721
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sec13
• Ensembl ID: ENSMUSG00000030298
• Aliases: Sec13, 1110003H02Rik, Sec13l1, Sec13r
• Description: SEC13 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:99832]

Sequence

>retro_mmus_3443
ATGGTGTCAGTAATTAACACTGTGGACACCTCTCATAGGAACCTGATCCATGATGCACAGATGGACTTATTATGGCACCT
GCCTATCAACCTGTTCCTCAGATAGGTCCGTCAAAATTTTTGATGTGTGAAAGGGAGGGCAGATCCTCATGGAAGACCTC
AAAGGACATGAGGGACCAGTGTGGCAAGTTGCCTGGGCCCATCCCATGTATGGCAATATCTTGGCCTCCTGTTCCTTTGA
CTGGCAAGTCATTATCTGGAAGAAGAAGAAGAAAAAAAAAAACGGCACTTGGGAGAAGACCTATGAACTCTCAGGACATG
ACTCCTCAGTGGACTCTGTTTGCTGGGCCCCTCATTACAGTGACCTGATCCTGGCCTGTGGGAGTTCACATGGGGCCACC
TCACTGCTGACCTATACAGGGGAAGGCCAGTGGGAAGTGAAGAAGATTAACAAGGCTCACATAATTAGTTGTAATGCTGT
CAGTTGGGCACTGGCTTTAGGCCTGGAAGTCTTATAGACCAACCATTAGGATGGAAACCCAATTGCATTGAGAAGTTTGC
ATCAGGTGGCTGTGACAGCCTCATCAACATATGGAAGGAAGAGGAAAATGGTCAGCTGAAAGATGTTCGAAGGTTAGAAG
CACAAAGCGACTCCGTTCAAGGCATTGCTTGGACCCCCTCCATTGGCTTGCCCACCAGCACCATTACGAGCTGCTCTTAG
GATGGCCAAGTGTTTATTTTGACCTGCCATGATGCCTCGGGCAGTATGTGGTCACCCAAACTTCTATACAAGTTCAATGA
CGTTGTGCGGCACGTGAACTGGTCCACCACAGCGAACCTCCTA

Alignment

ORF - retro_mmus_3443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.97 %
• Parental protein coverage: 86.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVSVMNTVDTSHEDMIHDAQMD-YYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPM
          MVSV.NTVDTSH...IHDAQMD.YYGT.L.TCSSDRSVKIFDV..GGQIL..DL.GHEGPVWQVAWAHPM
Retrocopy MVSVINTVDTSHRNLIHDAQMD>YYGTCLSTCSSDRSVKIFDV*KGGQILMEDLKGHEGPVWQVAWAHPM

Parental  YGNILASCSYDRKVIIWKEEN----GTWEKTHEHSGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYT
          YGNILASCS.D..VIIWK.......GTWEKT.E.SGHDSSV.SVCWAPH...LILACGSS.GA.SLLTYT
Retrocopy YGNILASCSFDWQVIIWKKKKXXXXGTWEKTYELSGHDSSVDSVCWAPHYSDLILACGSSHGATSLLTYT

Parental  GEGQWEVKKINNAHTIGCNAVSWAPAVV-PGSLIDQPSGQKPNYIKKFASGGCDNLIKLWREEEDGQWKE
          GEGQWEVKKIN.AH.I.CNAVSWA.A...PGSLIDQP.G.KPN.I.KFASGGCD.LI..W.EEE.GQ.K.
Retrocopy GEGQWEVKKINKAHIISCNAVSWALALG<PGSLIDQPLGWKPNCIEKFASGGCDSLINIWKEEENGQLKD

Parental  EQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASGNMWSPKLLHKFNDVVWHVSWSITA
          ...LEA.SD.V...AW.PSIGLPTSTI.SCS.DG.VFI.TC.DASG.MWSPKLL.KFNDVV.HV.WS.TA
Retrocopy VRRLEAQSDSVQGIAWTPSIGLPTSTITSCS*DGQVFILTCHDASGSMWSPKLLYKFNDVVRHVNWSTTA

Parental  NIL
          N.L
Retrocopy NLL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	35.72 RPM
SRP007412_cerebellum	0.00 RPM	32.22 RPM
SRP007412_heart	0.03 RPM	40.28 RPM
SRP007412_kidney	0.02 RPM	53.05 RPM
SRP007412_liver	0.00 RPM	39.38 RPM
SRP007412_testis	0.00 RPM	46.06 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3443 was not detected

EST

No EST(s) were mapped for retro_mmus_3443 retrocopy.

TSS

No TSS is located nearby retro_mmus_3443 retrocopy 5' end.

Lab

retro_mmus_3443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3443 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443 ,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,